Inside Canada's chaotic response to avian flu

Jelmer Wiersma's poultry farm near Cudworth, Sask. Wiersma lost his entire flock of nearly 90,000 birds in the fall of 2022 after some of his turkeys tested positive for avian influenza (Allison Bamford / CTV News)

Editor's note: This story is a collaboration between the Investigative Journalism Foundation (IJF) and CTV National News.

Cora Scheele knew something was wrong with the chickens.

On a normal day, the barns on the Scheeles’ farm in central Alberta pulse with life. But on a morning in April 2022, something was different. “The birds were kind of lame and had no energy,” Scheele said.

And then they started to die.

Within two days, every single bird in one of her five barns was dead, victims of a wave of avian influenza that has ravaged Canada’s poultry farms and wild birds alike.

The Scheeles called in the Canadian Food Inspection Agency (CFIA) which quarantined their farm and euthanized the birds in the remaining four barns to stop the spread of the virus. Altogether, roughly 37,000 birds were killed.

“You take them out of their misery, and that’s the only thing you can do,” said Arjan Scheele, Cora’s husband. “You cannot stop it.”

For years, Canadian farmers and government agencies have waged a fierce battle against the new wave of avian flu, which experts say is much more transmissible than previous variants of the virus.

Now, newly uncovered documents reveal the CFIA and industry were caught unprepared for the outbreak, which overwhelmed the agency’s resources and forced it to rely on third-party contractors who sometimes broke bio-security rules meant to keep the virus in check.

The IJF and CTV News have reviewed thousands of pages of CFIA documentation about their response to the current outbreak, including field reports, manuals on preferred killing methods, internal correspondence and dozens of invoices.

The records, which were obtained via access to information law by animal-rights group Animal Justice, paint a picture of the CFIA’s struggle to contain a massive outbreak of avian flu in which more than 11 million Canadian farm birds were killed.

Internally, top CFIA officials described the industry, and the agency, as being unprepared for such an outbreak. At times, inspectors described running out of carbon dioxide (CO2) gas — the preferred tool for euthanizing large numbers of birds. CFIA employees sometimes arrived at farms where many birds were already dead.

They also relied heavily on private companies, the documents said, who sometimes failed to follow bio-security protocols meant to stop the spread of the virus.

“CFIA has taken the lead to date because industry was not prepared,” wrote CFIA Atlantic regional veterinary officer Dr. Margaret McGeoghegan in an October 2022 email to colleagues.

“However, it is unreasonable to think that it is sustainable long-term,” she continued. “And in reality it is all hands on deck. CFIA is leading but is leaning heavy on industry for help particularly with manpower .... I am sorry to deliver such a blunt message but it is the reality.”

Scott Rattray, the CFIA’s associate vice president of operations, said in an interview there were times during the outbreak when 20 to 25 new infected premises were being reported every week.

“It's been the largest animal health emergency that this country has ever had to face,” Rattray said.

Stakeholders interviewed by the IJF and CTV News say the agency’s challenges are not wholly unexpected given how contagious the latest strain of the flu is.

“There’s not a country in the world that has the infrastructure, the veterinary power or the human resources and the funding to adequately face what we’ve been facing. There is none,” said Dr. Jean-Pierre Vaillancourt, a professor of veterinary epidemiology at the University of Montreal.

But he and other experts interviewed for this story say the reports should raise alarm bells about Canada’s preparedness for such epidemics.

“We make this mistake so many times,” said Dr. Timothy Sly, an epidemiology professor at Toronto Metropolitan University. “We wait until the wolf is in the barn, and then we figure out how to get it out.”

Toll of the outbreak

In October 2022, a farmer in the Ottawa Valley named Gerry Oleynik called the CFIA to his farm after a bird tested positive for avian flu.

Oleynik’s farm was not typical: he raised a number of exotic birds like ornamental waterfowl, macaws and swans.

The CFIA’s report from Oleynik’s farm says they had to use bolt guns to kill birds. When Oleynik returned, he said the scene was terrifying.

“There was blood all over in all the pens, blood scattered on the walls, on the floor there were heads of animals and birds here and there. There were some live birds that they didn’t destroy that we found that we had to destroy,” Oleynik said. He said the experience was traumatizing for him, his wife and their son, who raised some of those birds as personal pets.

“It was either you let (the CFIA) come in and kill everything and we give you some compensation, or you stay under quarantine, and everything might die a horrible death and you get no compensation at all. So we didn’t really have a choice but to let them do the right thing and come in and do this. It broke our hearts. We’re still not over it. But it was the right thing to do,” Oleynik said.

Across Canada, farmers like Oleynik were all facing similar heartbreak as the disease threatened their livelihoods.

And the CFIA was scrambling to be able to keep up with the volume of the work.

Since December 2021, the CFIA has recorded more than 400 outbreaks at poultry farms across all provinces and territories and destroyed more than 11 million birds.

That has taken a massive effort from CFIA staff. By March 2024, the agency estimated it had spent more than $94 million to respond to the avian flu.

Beyond the monetary expense, Rattray said that work took a serious mental-health toll on CFIA employees, contractors and farmers themselves.

Farmers, Rattray said, are compensated when the CFIA orders the destruction of their animals. But some farmers, like Oleynik, say the amount paid out by CFIA doesn’t always cover the cost of replacing the birds or the subsequent disinfection that farms must perform.

“It can't be understated the impact that this can have on producers when you're affecting your livelihood. In some really unfortunate cases, we were dealing with backyard flocks. These were like pets to people. These were difficult emotional situations,” Rattray said.

Contractor troubles

Since the start of the outbreak, the CFIA has paid more than $80 million to third-party contractors who perform work such as disposing of diseased bodies of birds and cleaning farms.

Those contractors did not always do their job correctly. In January 2023, a CFIA audit found “recurring issues” with a Chilliwack, B.C.-area company hired for “depopulation assistance.”

The issues included donning and doffing protective equipment in the wrong places, not adequately disinfecting clothing and removing protective equipment while in the “hot zone” where the virus is most active.

Those measures are essential, Vaillancourt said, because the latest strain of avian flu spreads incredibly quickly and easily, including through trace amounts of blood or feces from infected birds. And farming contractors, Vaillancourt said, may visit multiple farms in a given week, meaning they could become vectors for spreading the virus.

The Scheeles said they also had frustrations with the contractor who disposed of bodies on their farm.

After the CFIA had finished euthanizing birds in their five barns, the Scheeles said they were told to wait for a team from a private company contracted by the CFIA.

But that team, Arjan Scheele said, did not arrive until almost two weeks after the outbreak began and more than a week after the CFIA had finished euthanizing the last of their birds.

The result was that tens of thousands of corpses were left to decompose in the Scheeles’ barns.

“That was a big problem because now it was early April, so it was still cold, but the dead birds were all in the barn,” Cora said. She tried to keep the barns as cold as she should. But the rotting continued.

“You can imagine, it was in there for 14 days, and you start smelling something that’s not too nice,” she said.

The CFIA’s Rattray said in an interview that he was aware some contractors had violated bio-security rules.

“We were able to respond to those so that we were able to mitigate the risk before, you know, anything left the premises that could have spread it further,” Rattray said.

“We take it very seriously, because we understand the risks.”

Killing methods

Money and staffing were not the CFIA’s only problems.

At one point, the CFIA’s notes say it was having “significant difficulty” in obtaining key resources, including the CO2 gas it normally uses to euthanize birds in barns.

Rattray said part of that shortage was because the CFIA was competing for a limited supply of CO2 with the beverage industry.

Suffocation via CO2 gas, Vaillancourt said, is the preferred method of destroying birds because it is relatively quick and painless. The CFIA says using CO2 gas is ideal for “both efficiency and the physical and mental health of responders.”

The shortages, though, forced the CFIA to sometimes use other methods, including shooting birds with bolt guns or a technique called “cervical dislocation.”

Vaillancourt said such methods are more onerous for workers and potentially more uncomfortable for birds.

“You need a battalion. You need 25, 30 people. And that is a big bio-security challenge because they need to leave that place,” Vaillancourt said.

Briefing notes reveal that problems with securing CO2 pushed the agency to consider other options for euthanizing birds.

Some of those were disastrous.

In October 2022, the CFIA retained a Virginia-based company to experiment with using nitrogen-based foam to suffocate birds as an alternative to CO2. They tested the foam on a barn full of birds that had been exposed to avian flu but had not yet tested positive.

The experiment, according to the CFIA, was a “complete failure.” The foam failed to kill the birds instantly, instead causing them to “stampede” to one side of the barn. The CFIA team on site then had to “manually euthanize almost the entire barn” of the half-dead birds, something the agency said was exhausting for staff.

The report pointed blame at the company saying the company “had never actually completed destruction on a full-sized poultry facility” using foam.

“Companies completing Humane Destruction need to be thoroughly audited,” the report said.

Rattray said the foam experiment was a “valuable exercise” because it showed there could be “some promise” in such a technique.

“But, because it didn't meet our animal welfare standards, it wasn't something that we adopted,” Rattray said.

Camille Labchuk, an animal-rights lawyer and the executive director of Animal Justice, the group that obtained the records, says she was disturbed by reading that report, which did not outline exactly how many birds had to be manually killed.

“It turns my stomach to learn what these birds endured during what was essentially a test kill,” Labchuck said.

Foam was not the only option the agency seems to have explored. One package of documents suggests the CFIA was also discussing killing birds through “ventilation” — sealing off oxygen so that birds gradually suffocate.

That method is practised in the United States but is only used in “exceptional” circumstances in the European Union. It is controversial among animal-rights activists because of the pain it causes birds, which can take days to suffocate.

The CFIA eventually decided against endorsing that method.

Rattray said the CFIA was facing calls from some processors who wanted to explore ventilation during CFIA shortages, but said the agency opposed it.

“The only time that it would ever be considered to be used is if there was an established link and concern that this could become a human transmission issue,” Rattray said.

Labchuck said she was alarmed to learn they even considered it.

“We urge them not to. We urge them to consult with animal welfare experts on the methods that are considered to cause the least suffering to birds regardless of the costs,” Labchuck said.

Changing times

The devastation wreaked by avian flu has some calling for wholesale changes in how farmers and governments prepare.

Unlike France and other countries, Vaillancourt said, Canadian farmers generally don’t vaccinate domestic livestock against avian flu. He says that is because Canada is considered too small a market for pharmaceutical companies to conduct large-scale trials. And the CFIA, Vaillancourt said, doesn’t accept vaccination test results from other countries.

Vaillancourt says it is time to rethink that logic, particularly in areas like B.C.’s Fraser Valley, where multiple converging flyways for migratory birds create a hotspot for infections.

“You have a valley there that is designed for epidemics,” Vaillancourt said.

Rattray said the CFIA is looking at research on new avian flu vaccines in Europe. “These methods haven't been approved. But it is something that perhaps one day in the future will be available to us,” he said.

Avian flu is still present in Canada. As of Nov. 1, there were only 11 active infections in the country, almost all of them in B.C.

But rates have come down since the initial wave of infections in 2021 and 2022.

Farmers like Oleynik are hoping it stays that way.

“The fear is always there that avian flu is going to come back,” Oleynik said. “We always think about it, that we’re going to get hit.”

With CTV National News files from Allison Bamford